使用star-fusion软件分析融合gene，人和小鼠在官网已有构建好的参考基因组lib，可以下载直接使用。网站如下：https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/

对于非模式物种，构建参考基因组lib，可参考https://github.com/NCIP/ctat-genome-lib-builder/wiki

需要4个文件，fa、gtf、Pfam-A.hmm（/TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/database/pfam/Pfam-A.hmm）、dfam（https://dfam.org/releases/current/families/Dfam.hmm.gz，使用全库可能会报错，可以使用物种的Dfam库https://dfam.org/releases/current/infrastructure/dfamscan/）

构建

export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/star-fusion_1.9.0/bin:$PATH
perl /TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/star-fusion_1.9.0/lib/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl \
  --genome_fa /TJPROJ13/GB_TR/PJ_AI/AI_genome/animal/ensembl_97_ovis_aries_oar_v3_1_toplevel/Sequence/WholeGenomeFasta/genome.fa \
  --gtf /TJPROJ13/GB_TR/PJ_AI/AI_genome/animal/ensembl_97_ovis_aries_oar_v3_1_toplevel/Annotation/Genes/genome.gtf \
  --pfam_db /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/database/pfam/Pfam-A.hmm \
  --dfam_db /TJPROJ7/GB_TR/PUBLIC/database/ovis_aries_dfam/ovis_aries_dfam.hmm \

融合基因分析测试

export PYTHONPATH=""
unset PERL5LIB
export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/star-fusion_1.9.0/bin:$PATH
mkdir -p Ctrl_2
STAR-Fusion --genome_lib_dir 绝对路径/ctat_genome_lib_build_dir --left_fq Ctrl_2_1.clean.fq.gz --right_fq Ctrl_2_2.clean.fq.gz --examine_coding_effect --extract_fusion_reads --FusionInspector inspect --denovo_reconstruct --CPU 4 -O Ctrl_2 --tmpdir Ctrl_2/tmp --min_junction_reads 2 --min_sum_frags 2